Sequence similarities between large subunit ribosomal RNA gene intervening sequences from different Helicobacter species

Hurtado, Ana; Clewley, Jonathan P.; Linton, Dennis; Owen, Robert J.; Stanley, John R.

doi:10.1016/s0378-1119(97)00158-3

Cited by 26 publications

(11 citation statements)

References 27 publications

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“…The presence of IVSs in helicobacter 16S and 23S rRNA genes has been reported previously (26,33), and they are known to occur in other prokaryotes, such as some Enterobacteriaceae (45 Bacterial taxonomy or systematics deals with classification, nomenclature, and identification (11). Classification deals with the consistent arrangement of like taxa into groups.…”

Section: Discussionmentioning

confidence: 99%

Discordant 16S and 23S rRNA Gene Phylogenies for the Genus Helicobacter : Implications for Phylogenetic Inference and Systematics

et al. 2005

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Analysis of 16S rRNA gene sequences has become the primary method for determining prokaryotic phylogeny. Phylogeny is currently the basis for prokaryotic systematics. Therefore, the validity of 16S rRNA genebased phylogenetic analyses is of fundamental importance for prokaryotic systematics. Discrepancies between 16S rRNA gene analyses and DNA-DNA hybridization and phenotypic analyses have been noted in the genus Helicobacter. To clarify these discrepancies, we sequenced the 23S rRNA genes for 55 helicobacter strains representing 41 taxa (>2,700 bases per sequence). Phylogenetic-tree construction using neighbor-joining, parsimony, and maximum likelihood methods for 23S rRNA gene sequence data yielded stable trees which were consistent with other phenotypic and genotypic methods. The 16S rRNA gene sequence-derived trees were discordant with the 23S rRNA gene trees and other data. Discrepant 16S rRNA gene sequence data for the helicobacters are consistent with the horizontal transfer of 16S rRNA gene fragments and the creation of mosaic molecules with loss of phylogenetic information. These results suggest that taxonomic decisions must be supported by other phylogenetically informative macromolecules, such as the 23S rRNA gene, when 16S rRNA gene-derived phylogeny is discordant with other credible phenotypic and genotypic methods. This study found Wolinella succinogenes to branch with the unsheathed-flagellum cluster of helicobacters by 23S rRNA gene analyses and whole-genome comparisons. This study also found intervening sequences (IVSs) in the 23S rRNA genes of strains of 12 Helicobacter species. IVSs were found in helices 10, 25, and 45, as well as between helices 31 and 27. Simultaneous insertion of IVSs at three sites was found in H. mesocricetorum.

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Section: Discussionmentioning

confidence: 99%

Discordant 16S and 23S rRNA Gene Phylogenies for the Genus Helicobacter : Implications for Phylogenetic Inference and Systematics

et al. 2005

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“…They seem to be identical or highly similar within a Helicobacter species and interspecies similarities also exist (Hurtado et al, 1997). The insert usually starts in the same region.…”

Section: Insertion Sequences In the 16s Rrna Genementioning

confidence: 92%

“…Insertion sequences have been demonstrated to be rather common in both the 16S and 23S rRNA genes in Helicobacter species (Hurtado et al, 1997). They seem to be identical or highly similar within a Helicobacter species and interspecies similarities also exist (Hurtado et al, 1997).…”

Section: Insertion Sequences In the 16s Rrna Genementioning

confidence: 99%

Extension of the species Helicobacter bilis to include the reference strains of Helicobacter sp. flexispira taxa 2, 3 and 8 and Finnish canine and feline flexispira strains

Hänninen

Kärenlampi

Koort

et al. 2005

International Journal of Systematic and Evolutionary Microbiology

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The evolution and taxonomy of enterohepatic Helicobacter species with flexispira morphology were studied by a polyphasic approach including phenotypic characterization, analysis of 16S rRNA and ureB gene sequences and dot-blot DNA–DNA hybridization of whole genomic DNA. In addition, available phylogenetic data on the HSP60 gene were used in the analysis. The study included 14 Finnish canine and feline flexispira strains, the reference strains of Helicobacter sp. flexispira taxa 2, 3 and 8 and Helicobacter bilis ATCC 51630T. Phenotypically, all canine and feline strains were similar to H. bilis. Analysis of 16S rRNA gene sequences of these strains revealed a similarity of 97–99·5 %. Similarity of ureB nucleotide and amino acid sequences within the studied flexispira group was 97–100 % and 99–100 %, respectively, revealing close relatedness. ureB sequences of Helicobacter hepaticus had only 64–66 % similarity to the flexispira group. The similarity to Helicobacter trogontum was 81·5–82·1 %. High levels of DNA–DNA hybridization between the strains were found in dot-blot tests. Polyphasic analysis of the phenotypic and genotypic characteristics of the Finnish flexispira strains and the reference strains of taxa 2, 3 and 8 showed that they differed from other Helicobacter species and are members of the previously described species H. bilis. In addition, canine strain F56 differed in all phylogenetic analyses from the H. bilis group and probably represents a novel Helicobacter species.

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“…The presence of IVSs, without any proven function in stable rRNA genes, is surprising and may have implications regarding the evolution of rRNA transcription units. IVSs are distributed sporadically among the bacteria, having been identified in members of the Enterobacteriaceae (8,23,38), Rhizobiaceae (37), Rickettsiaceae (1), and Leptospiraceae (31) families and in the genera Campylobacter (14,19,41) and Helicobacter (13,18). It has also been shown that the distribution of IVSs among the several copies of rRNA operons is heterogeneous.…”

mentioning

confidence: 99%

Distribution of Intervening Sequences in the Genes for 23S rRNA and rRNA Fragmentation among Strains of the Salmonella Reference Collection B (SARB) and SARC Sets

Miller

Sanderson

2000

J Bacteriol

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Intervening sequences (IVSs) occur sporadically in several bacterial genera in the genes for 23S rRNA at relatively conserved locations. They are cleaved after transcription and lead to the presence of fragmented rRNA, which is incorporated into the ribosomes without religation but is nevertheless functional. The fragmentation of rRNA and the number of IVSs in all 72 strains of the Salmonella Reference Collection B set and 16 strains of the Salmonella Reference Collection C set, which have been established on the basis of multilocus enzyme electrophoresis (MLEE), were analyzed in the present study. Fragmentation of 23S rRNA was restricted to conserved cleavage sites located at bp 550 (helix 25) and bp 1170 (helix 45), locations where IVSs have been reported. Random cleavage at sites where IVSs could not be detected was not seen. Uncleaved IVSs were not detected in any case; thus, the IVSs invariably led to rRNA fragmentation, indicating a strong selection for maintenance of RNase III cleavage sites. The distribution of the number of IVSs carried by the different strains in the seven rrl genes is diverse, and the pattern of IVS possession could not be related to the MLEE pattern among the various Salmonella strains tested; this indicates that the IVSs are frequently exchanged between strains by lateral transfer. All eight subspecies of the genus Salmonella, including subspecies V represented by Salmonella bongori, have IVSs in both helix 25 and helix 45; this indicates that IVSs entered the genus after its divergence from Escherichia coli (more than 100 million years ago) but before separation of the genus Salmonella into many forms or that they were in the ancestor but have been lost from Escherichia.

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Sequence similarities between large subunit ribosomal RNA gene intervening sequences from different Helicobacter species

Cited by 26 publications

References 27 publications

Discordant 16S and 23S rRNA Gene Phylogenies for the Genus Helicobacter : Implications for Phylogenetic Inference and Systematics

Discordant 16S and 23S rRNA Gene Phylogenies for the Genus Helicobacter : Implications for Phylogenetic Inference and Systematics

Extension of the species Helicobacter bilis to include the reference strains of Helicobacter sp. flexispira taxa 2, 3 and 8 and Finnish canine and feline flexispira strains

Distribution of Intervening Sequences in the Genes for 23S rRNA and rRNA Fragmentation among Strains of the Salmonella Reference Collection B (SARB) and SARC Sets

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